I gave two seminars at @embl.org Heidelberg these days: One about using LLMs via #biabob for #BioImageAnalysis and one about how LLMs impact BioImage #DataScience
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
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scads.github.io/llm-bia-2025
AI-assisted cherry picking 🍒 using
next gen #biabob 🚀 #sneakpreview
New in #biabob 0.29.0: Code insertions in @jupyter.org Cells! 🥳
If you know how to start your image analysis, and how to visualize the results, just put %bob in between and let the AI do the hard coding work. Also provide hints as comments to guide the AI 😉
github.com/haesleinhuep...
#biabob 0.28.0 is out and it comes with support for OpenAI's codex-mini model. I also enabled its vision-support. With this, you can turn screenshots of user-interfaces into functional code - directly within your Jupyter notebook 🤯
github.com/haesleinhuep...
#biabob 0.27.0 brings support for @openrouter.bsky.social. With this you can access many of your favorite models such as Claude 3.7 Sonnet, GPT-4o, Gemini, ... via the same provider and only pay for one account🚀
Fun fact: #biabob knows how to forward a question to an LLM 😄
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It was a week of #LLM model releases. 😃
I just tried the most recent GPT 4.5-preview and Claude 3.7 Sonnet for BioImage Analysis Code Generation in Jupyter Notebooks and they work out of the box in #biabob 🔬🖥️🚀
github.com/haesleinhuep...
A screenshot of the code bia-bob generated after being tasked to use Astronomy specific libraries.
A screenshot of the code bia-bob generated after being tasked to write Python code always encapsulating code in functions.
A screenshot of the code bia-bob generated after being tasked to write Python code with Finnish variable names.
A screenshot of the code bia-bob generated after being tasked to write unnecessarily complicated Python code.
#biabob, the AI-based code generator for Jupyter Notebooks, can now be configured to generate code for other scientific domains🔭, coding-styles 🎭 and languages🗣️. Handle with care, as you can also use this to do stupid things. 😉 Feedback welcome🚀
pip install bia-bob==0.26.0
github.com/haesleinhuep...
Thanks! 🥰
Correct! Since version 0.18.0, #biabob remembers which model you used last time. This might be useful if you prefer working with claude 3.5 sonnet (like I do). It will forget this every time you update #biabob and fall back to the historical default model gpt4-o.
github.com/haesleinhuep...
A little #milestone for the #biabob project:
💯 Github Stars ⭐⭐⭐ 🚀
I'm happy to see the growing community using #biabob as
#BioImageAnalysis Coding Assistant in Jupyter.
I would love to learn more about what people use it for! Feel free to share screenshots below 😃
github.com/haesleinhuep...
Voilà! #gitbob and #biabob were updated to support #pixtral, the vision model from the French mistral.ai #LLM provider. It also comes with a free tier 🇫🇷 🇪🇺 🎉
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Hi #biabob users,
there comes a new edit mode with the new 0.24.0 release: If you ask %%bob to modify code, it will update the current notebook cell. This should make AI-assisted iterative code modifications much smoother. 🤓
github.com/haesleinhuep...
[video shortened; Bob needs ~10 sec to respond]
If you use Python and Jupyter regularly to analyze scientific image data - and want to integrate AI into your coding workflow: Consider trying out #biabob, the LLM-based coding assistant tailored specifically for image analysis 🔬💻🤖
Feedback 💚ly welcome!
github.com/haesleinhuep...
My slides about #BioImageAnalysis using #LLMs, also featuring the multi-lingual tools #clij, #clesperanto and #biabob are available #openaccess 🔬🖥️🗣️🔓
Big thanks Artemiy Golden and #iMOL Frankfurt for hosting me!
zenodo.org/records/1078...
